Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 161 of 172
Found at i:52760671 original size:63 final size:63
Alignment explanation
Indices: 52760598--52760723 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
52760588 ATAATAATAT
* *
52760598 TAATATTAATAATATGAAAATAACAAGGATATTTAGCTAAAAAAATGAAAAACAAAACGAAAA
1 TAATATTAATAATATGAAAATAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAA
52760661 TAATATTAATAATATGAAAATAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAA
1 TAATATTAATAATATGAAAATAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAA
52760724 CAGGACTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (63 bp):
TAATATTAATAATATGAAAATAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAA
Found at i:52760749 original size:63 final size:63
Alignment explanation
Indices: 52760604--52760749 Score: 170
Period size: 63 Copynumber: 2.3 Consensus size: 63
52760594 ATATTAATAT
* * * * * * *
52760604 TAATAATATGAAAATAACAAGGATATTTAGCTAAAAAAATGAAAAACAAAACGAAAATAATAT
1 TAATAATATAAAAAAAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAACAAGAC
* * *
52760667 TAATAATATGAAAATAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAACAGGAC
1 TAATAATATAAAAAAAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAACAAGAC
52760730 TAA-AAT-TAAACTAAAAACAA
1 TAATAATATAAA--AAAAACAA
52760750 AGTTGTGGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
61 3 0.04
62 3 0.04
63 67 0.92
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.19
Consensus pattern (63 bp):
TAATAATATAAAAAAAACAAGGATATTTAGATAAAAAAACGAAAAACAAAACGAAAACAAGAC
Found at i:52761564 original size:35 final size:35
Alignment explanation
Indices: 52761518--52761586 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
52761508 GGGTGTGTGA
52761518 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
52761553 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
52761587 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:52767202 original size:24 final size:24
Alignment explanation
Indices: 52767150--52767216 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
52767140 TTTATATATA
52767150 ATTTAT-TTATT-TTAAAAACTAT
1 ATTTATATTATTATTAAAAACTAT
**
52767172 ACATATATTATTATTAAAAA-TACT
1 ATTTATATTATTATTAAAAACTA-T
52767196 ATTTATA-TATTTATATAAAAA
1 ATTTATATTA-TTAT-TAAAAA
52767217 AATTTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 4 0.11
23 9 0.25
24 17 0.47
25 6 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTATATTATTATTAAAAACTAT
Found at i:52767261 original size:5 final size:5
Alignment explanation
Indices: 52767247--52767395 Score: 57
Period size: 5 Copynumber: 30.0 Consensus size: 5
52767237 ATTTTCCTAT
* * * *
52767247 TTAT- TTATA TTATA TTTTA TTATA TAACA TT-TA TTATA TT-TT TTAT-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * *
52767293 TTTTA TTTTA TTATA -TATTA CT-TA TTATA TTATT TTTTA TTATA -TATA
1 TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA
*
52767341 TCGTATA TTATCTA TTATA -TAT- TTATGTT TTATA TTATTCA TTATA TTAT-
1 T--TATA TTA--TA TTATA TTATA TTA--TA TTATA TTA-T-A TTATA TTATA
52767391 TTATA
1 TTATA
52767396 ATTTTAAAAT
Statistics
Matches: 111, Mismatches: 15, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
4 31 0.28
5 59 0.53
6 4 0.04
7 17 0.15
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:52767265 original size:42 final size:42
Alignment explanation
Indices: 52767218--52767328 Score: 102
Period size: 42 Copynumber: 2.6 Consensus size: 42
52767208 ATATAAAAAA
52767218 ATTTTATTTATCATATATTATTTTCCTA-TTTATTTATATTAT
1 ATTTTATTTATCATATATTATTTTCCTATTTTATTT-TATTAT
* **
52767260 ATTTTATTATATAACATTTATTATATTTTTTATTTTTATTTTATTAT
1 ATTTTATT-TAT--CATATATTAT-TTTCCTA-TTTTATTTTATTAT
* *
52767307 ATATTACTTAT--TATATTATTTT
1 ATTTTATTTATCATATATTATTTT
52767329 TTATTATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
41 3 0.05
42 15 0.26
43 3 0.05
45 9 0.16
46 8 0.14
47 12 0.21
48 7 0.12
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (42 bp):
ATTTTATTTATCATATATTATTTTCCTATTTTATTTTATTAT
Found at i:52767305 original size:37 final size:38
Alignment explanation
Indices: 52767244--52767337 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 38
52767234 ATTATTTTCC
*
52767244 TATTTATTTATATTATATTTTATTATATAACATTTATTA
1 TATTT-TTTATATTATATTTTATTATATAACACTTATTA
* **
52767283 TATTTTTTAT-TTTTATTTTATTATATATTACTTATTA
1 TATTTTTTATATTATATTTTATTATATAACACTTATTA
*
52767320 TATTATTTTTTATTATAT
1 TATT-TTTTATATTATAT
52767338 ATATCGTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 27 0.57
38 10 0.21
39 10 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (38 bp):
TATTTTTTATATTATATTTTATTATATAACACTTATTA
Found at i:52767311 original size:7 final size:7
Alignment explanation
Indices: 52767301--52767387 Score: 54
Period size: 7 Copynumber: 12.1 Consensus size: 7
52767291 ATTTTTATTT
52767301 TATTATA
1 TATTATA
52767308 TATTACT-
1 TATTA-TA
52767315 TATTATA
1 TATTATA
* *
52767322 TTATTTTT
1 -TATTATA
52767330 TATTATA
1 TATTATA
*
52767337 TATATCGTA
1 TAT-T-ATA
*
52767346 TATTATC
1 TATTATA
52767353 TATTATA
1 TATTATA
52767360 TATT-TA
1 TATTATA
* *
52767366 TGTTTTA
1 TATTATA
52767373 TATTAT-
1 TATTATA
52767379 TCATTATA
1 T-ATTATA
52767387 T
1 T
52767388 TATTTATAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
6 7 0.11
7 40 0.66
8 9 0.15
9 5 0.08
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (7 bp):
TATTATA
Found at i:52767612 original size:18 final size:18
Alignment explanation
Indices: 52767559--52767652 Score: 68
Period size: 18 Copynumber: 5.1 Consensus size: 18
52767549 TTTTACATAC
52767559 TTTTTATTTTATATATTAT
1 TTTTTATTTTATATA-TAT
**
52767578 TTTTT-TTAAATCAATATAT
1 TTTTTATTTTAT--ATATAT
*
52767597 TTTTTATTTTATATATAA
1 TTTTTATTTTATATATAT
* *
52767615 TTATTATTCTTTTATA-AT
1 TTTTTATT-TTATATATAT
52767633 TTTTT-TTGTTATTATATAT
1 TTTTTATT-TTA-TATATAT
52767652 T
1 T
52767653 GTATATTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
17 4 0.07
18 25 0.43
19 22 0.38
20 7 0.12
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTATTTTATATATAT
Found at i:52769687 original size:23 final size:23
Alignment explanation
Indices: 52769640--52769683 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
52769630 ATATTTATTT
52769640 TTATATCATAAAATTAAAAATAA
1 TTATATCATAAAATTAAAAATAA
*
52769663 TTATAT-ATTAAA-TAAAAATAA
1 TTATATCATAAAATTAAAAATAA
52769684 AATTTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TTATATCATAAAATTAAAAATAA
Found at i:52769999 original size:3 final size:3
Alignment explanation
Indices: 52769991--52770018 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52769981 TGAAGGATTT
52769991 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
52770019 CAACGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:52780955 original size:2 final size:2
Alignment explanation
Indices: 52780948--52781017 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
52780938 AGTAAAACTG
52780948 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52780990 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52781018 NATGTTATGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52784391 original size:2 final size:2
Alignment explanation
Indices: 52784384--52784457 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
52784374 NNNNNNNNNN
52784384 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
52784426 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
52784458 AATGTTAAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:52788085 original size:26 final size:26
Alignment explanation
Indices: 52788063--52788144 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 26
52788053 ATTCCGATAT
*
52788063 ATGGCTCTTCGTGAGCTTCCCGATTA
1 ATGGCTCTTTGTGAGCTTCCCGATTA
* * * *
52788089 AAGACTCTTTATGAGCTTCCTGATTA
1 ATGGCTCTTTGTGAGCTTCCCGATTA
*
52788115 ATGGCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTTGTGAGCTTCCCGATTA
52788141 ATGG
1 ATGG
52788145 TTCTCAGGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (26 bp):
ATGGCTCTTTGTGAGCTTCCCGATTA
Found at i:52788121 original size:52 final size:52
Alignment explanation
Indices: 52788043--52788141 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
52788033 CACACCGCAC
52788043 CTTTATGAGCATTCCGATATATGGCTCTTCGTGAGCTTCCCGATTAAAGACT
1 CTTTATGAGCATTCCGATATATGGCTCTTCGTGAGCTTCCCGATTAAAGACT
* *
52788095 CTTTATGAGC-TTCCTGAT-TAATGGCTCTTTGTGAGCTTCCTGATTAA
1 CTTTATGAGCATTCC-GATAT-ATGGCTCTTCGTGAGCTTCCCGATTAA
52788142 TGGTTCTCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 5 0.12
52 38 0.88
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (52 bp):
CTTTATGAGCATTCCGATATATGGCTCTTCGTGAGCTTCCCGATTAAAGACT
Found at i:52799163 original size:43 final size:42
Alignment explanation
Indices: 52799116--52799222 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
52799106 TCGATGACAT
*
52799116 TGTCCCAAACAGTGTCTTACACGAAATTGATT-A-ACTATGCCAA
1 TGTCCCAAACA-TGTCTTACACGAAATT--TTAATACAATGCCAA
* *
52799159 TGTCCCAAGCATGGTCTTACACGTAATTTTAATACAATGCCAA
1 TGTCCCAAACAT-GTCTTACACGAAATTTTAATACAATGCCAA
52799202 TGTCCCAAACATGATCTTACA
1 TGTCCCAAACATG-TCTTACA
52799223 TGTAATCATA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
41 2 0.04
42 3 0.05
43 51 0.91
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (42 bp):
TGTCCCAAACATGTCTTACACGAAATTTTAATACAATGCCAA
Found at i:52799747 original size:30 final size:28
Alignment explanation
Indices: 52799713--52799772 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
52799703 TTTTATTTCA
*
52799713 AATTTCAACCCCTCAATTTACATTTTTCTC
1 AATTT-AA-CCCTCAATTGACATTTTTCTC
* * *
52799743 AATTTAATCCTTAATTGACATTTTTGTC
1 AATTTAACCCTCAATTGACATTTTTCTC
52799771 AA
1 AA
52799773 AAATCACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 19 0.73
29 2 0.08
30 5 0.19
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (28 bp):
AATTTAACCCTCAATTGACATTTTTCTC
Found at i:52803191 original size:50 final size:50
Alignment explanation
Indices: 52803114--52803289 Score: 253
Period size: 50 Copynumber: 3.5 Consensus size: 50
52803104 TATGGCAACC
* * * *
52803114 AGTGATAAGTGATAGCTTCGACGACACTTATCTGGTCAAGGATAAGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
* *
52803164 AGTGATAAGTAATAGCTTCGGCTACACTTACCTGATCAAGGACAAGTGAA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
* *
52803214 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACAAATGACA
1 AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA-A
* *
52803265 AGTGAAAAGTGGTAGCTTCGGCTAC
1 AGTGATAAGTGATAGCTTCGGCTAC
52803290 CTGATCAGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (50 bp):
AGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAA
Found at i:52803303 original size:31 final size:31
Alignment explanation
Indices: 52803265--52803382 Score: 202
Period size: 31 Copynumber: 3.8 Consensus size: 31
52803255 ACAAATGACA
52803265 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
52803296 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
52803327 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
52803358 AGTGAATAA-TGGTAGCTTCGGCTAC
1 AGTGAA-AAGTGGTAGCTTCGGCTAC
52803383 AAGTGACAAG
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
31 81 0.98
32 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:52803471 original size:47 final size:46
Alignment explanation
Indices: 52803400--52803523 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 46
52803390 AAGTGATTTC
* * *
52803400 CGTATAAGACCATATCTGGCATATGACATCGGTGTGATATATGCTATT
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATG--ATT
* *
52803448 -GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATT
* * *
52803493 CGTGTAAGACCATAGCTGGGCTATGGCATCG
1 CGTATAAGACCATATCTGGGATATGGCATCG
52803524 ATATATGAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 3 0.05
46 26 0.39
47 37 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATT
Found at i:52803552 original size:42 final size:43
Alignment explanation
Indices: 52803494--52803608 Score: 171
Period size: 42 Copynumber: 2.7 Consensus size: 43
52803484 TATGTGATTC
*
52803494 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
52803536 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
52803578 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
52803609 GAAAACGAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:52807297 original size:35 final size:34
Alignment explanation
Indices: 52807212--52807297 Score: 84
Period size: 35 Copynumber: 2.5 Consensus size: 34
52807202 TTATATGCAT
* * **
52807212 AATAAATAAACATATATATTAATTTTTAGATATA
1 AATAAATAAAAATAAATATTAAAATTTAGATATA
* *
52807246 AA-ATAATCAAATATAAATATTAAAATTTATATTATA
1 AATA-AAT-AAAAATAAATATTAAAATTTAGA-TATA
52807282 AATAAATAAAAATAAA
1 AATAAATAAAAATAAA
52807298 CACACAAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
33 1 0.02
34 5 0.12
35 26 0.62
36 9 0.21
37 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (34 bp):
AATAAATAAAAATAAATATTAAAATTTAGATATA
Found at i:52829106 original size:68 final size:68
Alignment explanation
Indices: 52829031--52829167 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
52829021 ATCGTTGAGG
52829031 AATACCTACTAATTCATTCAATTACAAATCTTACTTATGCTATAAAGCATTAAAACTTACCATTT
1 AATACCTACTAATTCATTCAATTACAAATCTTACTTATGCTATAAAGCATTAAAACTTACCATTT
52829096 TAT
66 TAT
*
52829099 AATACCTACTAATTCATTCAATTACAAATCTTACTTATGTTATAAAGCATTAAAACTTACCATTT
1 AATACCTACTAATTCATTCAATTACAAATCTTACTTATGCTATAAAGCATTAAAACTTACCATTT
52829164 TAT
66 TAT
52829167 A
1 A
52829168 CACATATGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (68 bp):
AATACCTACTAATTCATTCAATTACAAATCTTACTTATGCTATAAAGCATTAAAACTTACCATTT
TAT
Found at i:52830001 original size:17 final size:17
Alignment explanation
Indices: 52829979--52830021 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
52829969 AGGTTTCTTA
52829979 TATTTTATATTTTATT-T
1 TATTTTAT-TTTTATTAT
52829996 TATTTTATTTTTATTAT
1 TATTTTATTTTTATTAT
*
52830013 GATTTTATT
1 TATTTTATT
52830022 AAAGAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTTTATTTTTATTAT
Found at i:52830751 original size:15 final size:15
Alignment explanation
Indices: 52830731--52830760 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52830721 TAAATCCCTC
52830731 CACACGACTTGGCCA
1 CACACGACTTGGCCA
52830746 CACACGACTTGGCCA
1 CACACGACTTGGCCA
52830761 TACAACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.40, G:0.20, T:0.13
Consensus pattern (15 bp):
CACACGACTTGGCCA
Found at i:52833719 original size:33 final size:33
Alignment explanation
Indices: 52833581--52833723 Score: 108
Period size: 33 Copynumber: 4.3 Consensus size: 33
52833571 TGGCCTAACC
* * *
52833581 ATGGTCTTACATTCGTAGTGCCATAACCTAGTT
1 ATGGTCTTACATTCATAATGCCATAACCCAGTT
* * *
52833614 ATGGTCTTATCA-TCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTCATAATGCCATAACCCAGTT
* ** * *** * *
52833647 ATGGTTTTACTTATAAATACTGCCATGGTCCAATA
1 ATGGTCTTAC--ATTCATAATGCCATAACCCAGTT
*
52833682 ATGGTCTTACATTCATAATGACATAACCCAGTT
1 ATGGTCTTACATTCATAATGCCATAACCCAGTT
52833715 ATGGTCTTA
1 ATGGTCTTA
52833724 TCCGTCAATT
Statistics
Matches: 80, Mismatches: 26, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
32 1 0.01
33 55 0.69
34 3 0.04
35 21 0.26
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTCATAATGCCATAACCCAGTT
Found at i:52836111 original size:14 final size:14
Alignment explanation
Indices: 52836089--52836118 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52836079 TATACTTAGT
52836089 TTAACTTTAATTAA
1 TTAACTTTAATTAA
*
52836103 TTAAGTTTAATTAA
1 TTAACTTTAATTAA
52836117 TT
1 TT
52836119 TAATCTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (14 bp):
TTAACTTTAATTAA
Found at i:52839108 original size:52 final size:48
Alignment explanation
Indices: 52839046--52839238 Score: 187
Period size: 47 Copynumber: 4.0 Consensus size: 48
52839036 GAAATGTGAT
* *
52839046 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
52839098 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * *
52839145 TACTGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATACGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * * *
52839191 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-GTATGTGATATGTG
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAG--TGTGATATGTG
52839239 ACTATGTGCA
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
46 26 0.22
47 53 0.44
48 10 0.08
50 1 0.01
51 1 0.01
52 29 0.24
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:52844398 original size:46 final size:46
Alignment explanation
Indices: 52844336--52844463 Score: 238
Period size: 46 Copynumber: 2.8 Consensus size: 46
52844326 AACTAGGCAT
*
52844336 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
52844382 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
*
52844428 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGG
52844464 GCGGGTTACA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.26
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
Found at i:52846834 original size:138 final size:137
Alignment explanation
Indices: 52846680--52846936 Score: 487
Period size: 138 Copynumber: 1.9 Consensus size: 137
52846670 ATTTAATATT
*
52846680 ATTGTTTTTTATTTTCGTGCATATCATTTGCTATTATTATTATTGCCTTCATTCCATTATTATTA
1 ATTGTATTTTATTTTCGTGCATATCATTTGCTATTATTATTATTGCCTTCATTCCATTATTATTA
52846745 TTGCTATTGCTATTTTTTTTTTGTTGTCCGTATTTTTATATATATTATTATTATTTAATATTATT
66 TTGCTATTGCTA-TTTTTTTTTGTTGTCCGTATTTTTATATATATTATTATTATTTAATATTATT
52846810 GTATTACA
130 GTATTACA
52846818 ATTGTATTTTATTTTCGTGCATATCATTTGCTATTATTATTATTGCCTTCATTCCATTATTATTA
1 ATTGTATTTTATTTTCGTGCATATCATTTGCTATTATTATTATTGCCTTCATTCCATTATTATTA
*
52846883 TTGCTATTGCTATTTTTTTTTGTTGTCCGTATTTTTATTTATATTATTATTATT
66 TTGCTATTGCTATTTTTTTTTGTTGTCCGTATTTTTATATATATTATTATTATT
52846937 AATGTCATTG
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
137 41 0.35
138 76 0.65
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (137 bp):
ATTGTATTTTATTTTCGTGCATATCATTTGCTATTATTATTATTGCCTTCATTCCATTATTATTA
TTGCTATTGCTATTTTTTTTTGTTGTCCGTATTTTTATATATATTATTATTATTTAATATTATTG
TATTACA
Found at i:52851059 original size:14 final size:14
Alignment explanation
Indices: 52851040--52851069 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52851030 TTTTATGTTG
*
52851040 AAAAAATATTTATA
1 AAAAAATATTAATA
52851054 AAAAAATATTAATA
1 AAAAAATATTAATA
52851068 AA
1 AA
52851070 TGATTGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAATATTAATA
Found at i:52861357 original size:13 final size:13
Alignment explanation
Indices: 52861339--52861394 Score: 67
Period size: 13 Copynumber: 4.0 Consensus size: 13
52861329 AAAATCATAT
52861339 GTCAATGCATAAA
1 GTCAATGCATAAA
*
52861352 GTCAATGGTGCTATAAT
1 GTCAA---TGC-ATAAA
52861369 GTCAATGCATAAA
1 GTCAATGCATAAA
52861382 GTCAATGCATAAA
1 GTCAATGCATAAA
52861395 TTAGATTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 22 0.59
14 3 0.08
16 3 0.08
17 9 0.24
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (13 bp):
GTCAATGCATAAA
Found at i:52863661 original size:42 final size:42
Alignment explanation
Indices: 52863615--52863695 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
52863605 GGAAATGGGC
* *
52863615 GTGTGCCCAAGTCGCGTGAGCCACACGGGCAAGGACATGAAT
1 GTGTGCCCAAGCCGCGTGAGCCACACGGGAAAGGACATGAAT
* * *
52863657 GTGTGCTCAGGCCGTGTGAGCCACACGGGAAAGGACATG
1 GTGTGCCCAAGCCGCGTGAGCCACACGGGAAAGGACATG
52863696 GGCATGTGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.15
Consensus pattern (42 bp):
GTGTGCCCAAGCCGCGTGAGCCACACGGGAAAGGACATGAAT
Found at i:52864633 original size:20 final size:20
Alignment explanation
Indices: 52864605--52864655 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
52864595 TCAACATTGC
* *
52864605 TCTGCTCTGTTCTATTATGT
1 TCTGTTCTGTTCTATTAGGT
* * *
52864625 TTTGTTCTGCTCTATTCGGT
1 TCTGTTCTGTTCTATTAGGT
52864645 TCTGTTCTGTT
1 TCTGTTCTGTT
52864656 TGAATTGTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.06, C:0.20, G:0.18, T:0.57
Consensus pattern (20 bp):
TCTGTTCTGTTCTATTAGGT
Found at i:52864684 original size:15 final size:15
Alignment explanation
Indices: 52864666--52864704 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
52864656 TGAATTGTGT
52864666 TGTTCTACTTTGTTC
1 TGTTCTACTTTGTTC
* *
52864681 TGTTTTGCTTTGTTC
1 TGTTCTACTTTGTTC
*
52864696 TGTTGTACT
1 TGTTCTACT
52864705 ACCTCTGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.15, G:0.18, T:0.62
Consensus pattern (15 bp):
TGTTCTACTTTGTTC
Found at i:52866333 original size:8 final size:9
Alignment explanation
Indices: 52866305--52866344 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
52866295 TAATGACAAT
52866305 AAATTATAA
1 AAATTATAA
52866314 AGAATT-TAA
1 A-AATTATAA
52866323 AAATTATAA
1 AAATTATAA
52866332 AAATTATAA
1 AAATTATAA
52866341 AAAT
1 AAAT
52866345 ACAAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.14
9 21 0.72
10 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:52866350 original size:17 final size:17
Alignment explanation
Indices: 52866305--52866351 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
52866295 TAATGACAAT
*
52866305 AAATTATAAAGAATTTAA
1 AAATTACAAA-AATTTAA
*
52866323 AAATTATAAAAATTATAA
1 AAATTACAAAAATT-TAA
52866341 AAA-TACAAAAA
1 AAATTACAAAAA
52866352 AATAACATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
AAATTACAAAAATTTAA
Found at i:52866819 original size:42 final size:42
Alignment explanation
Indices: 52866773--52866858 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
52866763 TTTAATTAAG
52866773 AATTCTGAATGAGAATTAAATTCTTGTATAATTTCCTTTGTA
1 AATTCTGAATGAGAATTAAATTCTTGTATAATTTCCTTTGTA
52866815 AATTCTGAATGAGAATTAAATTCTTGTATAATTTCCTTTGTA
1 AATTCTGAATGAGAATTAAATTCTTGTATAATTTCCTTTGTA
52866857 AA
1 AA
52866859 CCCTCAAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (42 bp):
AATTCTGAATGAGAATTAAATTCTTGTATAATTTCCTTTGTA
Found at i:52876773 original size:6 final size:6
Alignment explanation
Indices: 52876762--52876808 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
52876752 TCCTCTTATC
*
52876762 TTTTTA TTTTTA TTTTTTA TTTTTTA TTTTTA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTT
52876809 CAATTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 26 0.67
7 13 0.33
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:52876778 original size:7 final size:7
Alignment explanation
Indices: 52876757--52876803 Score: 64
Period size: 6 Copynumber: 7.0 Consensus size: 7
52876747 TTGAATCCTC
52876757 TTATCTTT
1 TTAT-TTT
52876765 TTA-TTT
1 TTATTTT
52876771 TTATTTT
1 TTATTTT
52876778 TTATTTT
1 TTATTTT
52876785 TTA-TTT
1 TTATTTT
52876791 TTA-TTT
1 TTATTTT
52876797 TTATTTT
1 TTATTTT
52876804 CATTTCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 18 0.49
7 16 0.43
8 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:52876780 original size:13 final size:14
Alignment explanation
Indices: 52876757--52876800 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 14
52876747 TTGAATCCTC
*
52876757 TTATCTTTTTATTT
1 TTATATTTTTATTT
52876771 TTAT-TTTTTATTT
1 TTATATTTTTATTT
52876784 TT-TATTTTTATTT
1 TTATATTTTTATTT
52876797 TTAT
1 TTAT
52876801 TTTCATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 5 0.18
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (14 bp):
TTATATTTTTATTT
Found at i:52880172 original size:31 final size:32
Alignment explanation
Indices: 52880131--52880193 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
52880121 TTATTTATAA
*
52880131 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
52880162 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
52880194 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:52881851 original size:26 final size:26
Alignment explanation
Indices: 52881812--52881867 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
52881802 TGATACAAAT
52881812 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
52881838 TGATAAT-GGTTTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
52881864 TGAT
1 TGAT
52881868 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:52892172 original size:26 final size:26
Alignment explanation
Indices: 52892143--52892195 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
52892133 TTTACAGTTT
52892143 TACCCATAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* * *
52892169 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
52892195 T
1 T
52892196 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:52893353 original size:12 final size:12
Alignment explanation
Indices: 52893336--52893370 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52893326 ATGTGCCGAA
**
52893336 TACTGTTATTGT
1 TACTGTTACCGT
52893348 TACTGTTACCGT
1 TACTGTTACCGT
52893360 TACTGTTACCG
1 TACTGTTACCG
52893371 ATTCGGTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
TACTGTTACCGT
Found at i:52893412 original size:45 final size:45
Alignment explanation
Indices: 52893348--52893458 Score: 177
Period size: 45 Copynumber: 2.5 Consensus size: 45
52893338 CTGTTATTGT
* *
52893348 TACTGTTACCGTTACTGTTACCGATTCGGTACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGTACTTTGTGTGTCGAA
* * *
52893393 TACTGTTACTATTACTGTTATCGATTCAGTACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGTACTTTGTGTGTCGAA
52893438 TACTGTTACTGTTACTGTTAC
1 TACTGTTACTGTTACTGTTAC
52893459 TGTTACTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGTACTTTGTGTGTCGAA
Found at i:52893449 original size:6 final size:6
Alignment explanation
Indices: 52893438--52893468 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
52893428 GTGTGTTGAA
52893438 TACTGT TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
52893469 CCGGATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:52893827 original size:54 final size:55
Alignment explanation
Indices: 52893698--52893835 Score: 140
Period size: 54 Copynumber: 2.5 Consensus size: 55
52893688 TATTAGACTA
* * *
52893698 TTACTGAATAACTGAA-TATTACTGAATAA-TTGATCATTACTGAATAACTGATTG
1 TTACTGAATAA-TTAACTGTTACTGAATAACTTAATCATTACTGAATAACTGATTG
* * * ** *
52893752 TCACTGAATGAA-TGACCGTTACTGAATAACTTAATTGTTACTGAATATCTGATT-
1 TTACTGAAT-AATTAACTGTTACTGAATAACTTAATCATTACTGAATAACTGATTG
*
52893806 TTACTGAATAATTAACTGTTACTGGATAAC
1 TTACTGAATAATTAACTGTTACTGAATAAC
52893836 CGATCAATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
53 3 0.04
54 42 0.63
55 22 0.33
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (55 bp):
TTACTGAATAATTAACTGTTACTGAATAACTTAATCATTACTGAATAACTGATTG
Found at i:52893829 original size:18 final size:18
Alignment explanation
Indices: 52893648--52893834 Score: 123
Period size: 18 Copynumber: 10.4 Consensus size: 18
52893638 TTATTATTAT
52893648 TGAATAATTGACTGTTAC
1 TGAATAATTGACTGTTAC
* * * *
52893666 CGGATAATTTACTGTTAT
1 TGAATAATTGACTGTTAC
* *
52893684 TGGAT-ATTAGACTATTAC
1 TGAATAATT-GACTGTTAC
* * *
52893702 TGAATAACTGAATATTAC
1 TGAATAATTGACTGTTAC
*
52893720 TGAATAATTGA-TCATTAC
1 TGAATAATTGACT-GTTAC
* * *
52893738 TGAATAACTGATTGTCAC
1 TGAATAATTGACTGTTAC
*
52893756 TGAATGAA-TGACCGTTAC
1 TGAAT-AATTGACTGTTAC
* *
52893774 TGAATAACTTAATTGTTAC
1 TGAATAA-TTGACTGTTAC
*
52893793 TGAAT-ATCTGA-TTTTAC
1 TGAATAAT-TGACTGTTAC
*
52893810 TGAATAATTAACTGTTAC
1 TGAATAATTGACTGTTAC
*
52893828 TGGATAA
1 TGAATAA
52893835 CCGATCAATT
Statistics
Matches: 133, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
17 19 0.14
18 97 0.73
19 17 0.13
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TGAATAATTGACTGTTAC
Found at i:52893905 original size:18 final size:18
Alignment explanation
Indices: 52893884--52893923 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52893874 AATAATTGAT
*
52893884 TGTTACCGAATAACTAAC
1 TGTTACCGAATAAATAAC
* *
52893902 TGTTACTGACTAAATAAC
1 TGTTACCGAATAAATAAC
52893920 TGTT
1 TGTT
52893924 CTGATTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTTACCGAATAAATAAC
Found at i:52913611 original size:76 final size:76
Alignment explanation
Indices: 52913485--52913637 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
52913475 CCACAACTCT
*
52913485 AAAATTAAGTTCCCATTGGTGTTCAATAAGGTAAGGCCGCCTACCAGGAAGCTGAAGACCACTTA
1 AAAATCAAGTTCCCATTGGTGTTCAATAAGGTAAGGCCGCCTACCAGGAAGCTGAAGACCACTTA
52913550 CAAGGCATCAA
66 CAAGGCATCAA
52913561 AAAATCAAGTTCCCATTGGTGTTCAATAAGGTAAGGCCGCCTACCAGGAAGCTGAAGACCACTTA
1 AAAATCAAGTTCCCATTGGTGTTCAATAAGGTAAGGCCGCCTACCAGGAAGCTGAAGACCACTTA
52913626 CAAGGCATCAA
66 CAAGGCATCAA
52913637 A
1 A
52913638 GCCTAACTTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (76 bp):
AAAATCAAGTTCCCATTGGTGTTCAATAAGGTAAGGCCGCCTACCAGGAAGCTGAAGACCACTTA
CAAGGCATCAA
Found at i:52924073 original size:15 final size:15
Alignment explanation
Indices: 52924053--52924086 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52924043 ATGAACATAA
*
52924053 AATATTAATAACAAT
1 AATATTAATAAAAAT
*
52924068 AATATTAGTAAAAAT
1 AATATTAATAAAAAT
52924083 AATA
1 AATA
52924087 AAAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATTAATAAAAAT
Found at i:52924103 original size:24 final size:25
Alignment explanation
Indices: 52924036--52924105 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
52924026 TAAAATTAGG
*
52924036 TAAAAA-AATGAACATAAAATATTAA
1 TAAAAATAAT-AATATAAAATATTAA
* *
52924061 TAACAATAATATTAGTAAAA-A-TAA
1 TAAAAATAATAATA-TAAAATATTAA
52924085 TAAAAATAAATAATATAAAAT
1 TAAAAAT-AATAATATAAAAT
52924106 TTGAAAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 14 0.39
25 14 0.39
26 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
TAAAAATAATAATATAAAATATTAA
Found at i:52924259 original size:3 final size:3
Alignment explanation
Indices: 52924251--52924284 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
52924241 GTTTAATAGT
*
52924251 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52924285 CGACGCGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:52924413 original size:3 final size:3
Alignment explanation
Indices: 52924407--52924588 Score: 76
Period size: 3 Copynumber: 60.3 Consensus size: 3
52924397 CATTAATAGG
* *
52924407 AAT AAT AAT -AT AGACT AAT AAT AAC AAT AAC AGA- AA- AAT AAT AA-
1 AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * *
52924451 AAT AAT AAT AAT AAT -AT AAT GAAT AAT GAC AAC AAT AAT -AT AAAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT
* * ** * *
52924496 AGT AAT AGA- AA- AAC AAT AAT AGA- AAT AGC AAC GAT AAT AAT AAAT
1 AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* * * *
52924541 AAT AAG AGT AAT AGT AAT AAT AAAT AAT AAT AAT AAT ATGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT
52924588 A
1 A
52924589 CTCTAAACGT
Statistics
Matches: 138, Mismatches: 24, Indels: 34
0.70 0.12 0.17
Matches are distributed among these distances:
2 15 0.11
3 103 0.75
4 18 0.13
5 2 0.01
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:52924584 original size:16 final size:15
Alignment explanation
Indices: 52924533--52924588 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
52924523 GCAACGATAA
*
52924533 TAATAAATAATAAGAG
1 TAAT-AATAATAATAG
* *
52924549 TAATAGTAATAATAAA
1 TAATAATAATAAT-AG
52924565 TAATAATAATAATATG
1 TAATAATAATAATA-G
52924581 TAATAATA
1 TAATAATA
52924589 CTCTAAACGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 8 0.24
16 25 0.76
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:52926559 original size:3 final size:3
Alignment explanation
Indices: 52926545--52926636 Score: 50
Period size: 3 Copynumber: 30.3 Consensus size: 3
52926535 ATGTATACCA
* * *
52926545 AAT AAT ACAT AAT AAT ATT AA- AAT AA- AAT AAT AAGT AAC AAT AGT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
* *
52926590 GAA- AAT AAT AAGT -AT AAT AAT AA- ATAT AAT GAT ATAT AAA AAT AAT
1 -AAT AAT AAT AA-T AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT
52926636 A
1 A
52926637 CTATATATAA
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
2 8 0.12
3 48 0.71
4 12 0.18
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:52926587 original size:26 final size:27
Alignment explanation
Indices: 52926544--52926597 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
52926534 TATGTATACC
* *
52926544 AAATAATACATAATAATA-TTAAAATA
1 AAATAATACATAACAATAGTGAAAATA
52926570 AAATAATA-AGTAACAATAGTGAAAATA
1 AAATAATACA-TAACAATAGTGAAAATA
52926597 A
1 A
52926598 TAAGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 15 0.62
27 8 0.33
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.26
Consensus pattern (27 bp):
AAATAATACATAACAATAGTGAAAATA
Found at i:52926608 original size:12 final size:11
Alignment explanation
Indices: 52926593--52926704 Score: 50
Period size: 12 Copynumber: 9.4 Consensus size: 11
52926583 CAATAGTGAA
52926593 AATAATAAGTAT
1 AATAATAA-TAT
52926605 AATAATAAATAT
1 AATAAT-AATAT
* *
52926617 AATGATATATAAA
1 AATAATA-AT-AT
*
52926630 AATAATACTAT
1 AATAATAATAT
*
52926641 ATATAAAAAGTAT
1 A-ATAATAA-TAT
52926654 -ATATATACACGTAT
1 AATA-ATA-A--TAT
52926668 AATAA-AATAT
1 AATAATAATAT
*
52926678 -ATACTAATATT
1 AATAATAATA-T
52926689 AATAATAAATAT
1 AATAAT-AATAT
52926701 AATA
1 AATA
52926705 GCGGTGAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
9 3 0.04
10 7 0.09
11 7 0.09
12 34 0.44
13 18 0.23
14 5 0.06
15 3 0.04
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (11 bp):
AATAATAATAT
Found at i:52926632 original size:18 final size:17
Alignment explanation
Indices: 52926591--52926660 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
52926581 AACAATAGTG
52926591 AAAATAATAAGTATA-ATA
1 AAAAT-ATAA-TATATATA
52926609 ATAAATATAATGATATATA
1 A-AAATATAAT-ATATATA
*
52926628 AAAATAATACTATATATA
1 AAAAT-ATAATATATATA
52926646 AAAAGTAT-ATATATA
1 AAAA-TATAATATATA
52926661 CACGTATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.16
18 25 0.56
19 13 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAATATAATATATATA
Found at i:52926727 original size:3 final size:3
Alignment explanation
Indices: 52926719--52926757 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
52926709 TGAAATAGGT
*
52926719 ATA ATA AT- ATA TTA GATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
52926758 TGTGAAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.88
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:52936246 original size:14 final size:14
Alignment explanation
Indices: 52936227--52936256 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52936217 TATTTTCAAG
52936227 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
52936241 ATAGATTCACGCAT
1 ATAGATTAACGCAT
52936255 AT
1 AT
52936257 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:52942793 original size:15 final size:15
Alignment explanation
Indices: 52942773--52942806 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52942763 ATGAACATAA
*
52942773 AATATTAATAACAAT
1 AATATTAATAAAAAT
*
52942788 AATATTAGTAAAAAT
1 AATATTAATAAAAAT
52942803 AATA
1 AATA
52942807 AAAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATTAATAAAAAT
Found at i:52942823 original size:24 final size:25
Alignment explanation
Indices: 52942756--52942825 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
52942746 TAAAATTAGG
*
52942756 TAAAAA-AATGAACATAAAATATTAA
1 TAAAAATAAT-AATATAAAATATTAA
* *
52942781 TAACAATAATATTAGTAAAA-A-TAA
1 TAAAAATAATAATA-TAAAATATTAA
52942805 TAAAAATAAATAATATAAAAT
1 TAAAAAT-AATAATATAAAAT
52942826 TTGAAAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 14 0.39
25 14 0.39
26 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
TAAAAATAATAATATAAAATATTAA
Found at i:52942926 original size:4 final size:4
Alignment explanation
Indices: 52942905--52942944 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
52942895 AAACTAATCT
*
52942905 ATAA A-AA AT-A AT-A ATAA ATAA ATAA ATAA ACAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
52942945 TTGAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:52943130 original size:3 final size:3
Alignment explanation
Indices: 52943124--52943295 Score: 56
Period size: 3 Copynumber: 57.3 Consensus size: 3
52943114 CATTAATAGG
* *
52943124 AAT AAT AAT -AT AGACT AAT AAT AAC AAT AAC AGA- AA- AAT AAT AA-
1 AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * *
52943168 AAT AAT AAT AAT AAT -AT AAT GAAT AAT GAC AAC AAT AAT -AT AAAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT
* * ** * *
52943213 AGT AAT AGA- AA- AAC AAT AAT AGA- AAT AGC AAC GAT AAT AAT AAAT
1 AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* * ** *
52943258 AAT AAG AGT AAT AGC AAT AAT AAT AAT ATGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
52943296 CTCTAAACGT
Statistics
Matches: 127, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
2 15 0.12
3 95 0.75
4 15 0.12
5 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:52943293 original size:31 final size:31
Alignment explanation
Indices: 52943227--52943285 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
52943217 ATAGAAAAAC
* *
52943227 AATAATAGAAATAGCAACGATAATAATAAAT
1 AATAAGAGAAATAGCAACAATAATAATAAAT
* *
52943258 AATAAGAGTAATAGCAATAATAATAATA
1 AATAAGAGAAATAGCAACAATAATAATA
52943286 TGTAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24
Consensus pattern (31 bp):
AATAAGAGAAATAGCAACAATAATAATAAAT
Found at i:52944819 original size:15 final size:15
Alignment explanation
Indices: 52944799--52944832 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52944789 ATGAACATAA
*
52944799 AATATTAATAACAAT
1 AATATTAATAAAAAT
*
52944814 AATATTAGTAAAAAT
1 AATATTAATAAAAAT
52944829 AATA
1 AATA
52944833 AAAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
AATATTAATAAAAAT
Found at i:52944849 original size:24 final size:25
Alignment explanation
Indices: 52944782--52944851 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
52944772 TAAAATAAGG
*
52944782 TAAAAA-AATGAACATAAAATATTAA
1 TAAAAATAAT-AATATAAAATATTAA
* *
52944807 TAACAATAATATTAGTAAAA-A-TAA
1 TAAAAATAATAATA-TAAAATATTAA
52944831 TAAAAATAAATAATATAAAAT
1 TAAAAAT-AATAATATAAAAT
52944852 TTGAAAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 14 0.39
25 14 0.39
26 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
TAAAAATAATAATATAAAATATTAA
Found at i:52944952 original size:4 final size:4
Alignment explanation
Indices: 52944931--52944970 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
52944921 AAACTAATCT
*
52944931 ATAA A-AA AT-A AT-A ATAA ATAA ATAA ATAA ACAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
52944971 TTGAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:52945156 original size:3 final size:3
Alignment explanation
Indices: 52945150--52945324 Score: 69
Period size: 3 Copynumber: 58.3 Consensus size: 3
52945140 CATTAATAGG
* *
52945150 AAT AAT AAT -AT AGACT AAT AAT AAC AAT AAC AGA- AA- AAT AAT AAT
1 AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * *
52945195 AA- AAT GAT AAT AAT AAT AAT AAT AAT AAT GAC AAC AAT AAT -AT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * ** * *
52945242 AGT AAT AGA- AA- AAC AAT AAT AGA- AAT AGC AAC GAT AAT AAT AAAT
1 AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* * ** *
52945287 AAT AAG AGT AAT AGC AAT AAT AAT AAT ATGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
52945325 CTCTAAACGT
Statistics
Matches: 130, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
2 13 0.10
3 103 0.79
4 12 0.09
5 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:52945209 original size:20 final size:20
Alignment explanation
Indices: 52945150--52945216 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
52945140 CATTAATAGG
*
52945150 AATAATAATATAGACTAATAAT
1 AATAATAAAAT-GA-TAATAAT
* *
52945172 AACAATAACA-GA-AA-AAT
1 AATAATAAAATGATAATAAT
52945189 AATAATAAAATGATAATAAT
1 AATAATAAAATGATAATAAT
52945209 AATAATAA
1 AATAATAA
52945217 TAATAATGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.29
18 4 0.11
19 2 0.05
20 13 0.34
22 8 0.21
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAATAAAATGATAATAAT
Found at i:52945322 original size:31 final size:31
Alignment explanation
Indices: 52945256--52945314 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
52945246 ATAGAAAAAC
* *
52945256 AATAATAGAAATAGCAACGATAATAATAAAT
1 AATAAGAGAAATAGCAACAATAATAATAAAT
* *
52945287 AATAAGAGTAATAGCAATAATAATAATA
1 AATAAGAGAAATAGCAACAATAATAATA
52945315 TGTAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24
Consensus pattern (31 bp):
AATAAGAGAAATAGCAACAATAATAATAAAT
Found at i:52946693 original size:5 final size:5
Alignment explanation
Indices: 52946683--52946708 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52946673 TATTTATTAA
52946683 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
52946709 TATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:52946716 original size:10 final size:10
Alignment explanation
Indices: 52946682--52946724 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
52946672 ATATTTATTA
52946682 ATAATTTAAT
1 ATAATTTAAT
*
52946692 TTAATTTAAT
1 ATAATTTAAT
* *
52946702 TTAATTTTAT
1 ATAATTTAAT
*
52946712 ATAATTAAAT
1 ATAATTTAAT
52946722 ATA
1 ATA
52946725 TCACATAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:52946716 original size:15 final size:15
Alignment explanation
Indices: 52946682--52946717 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52946672 ATATTTATTA
52946682 ATAATTTAATTTAAT
1 ATAATTTAATTTAAT
* *
52946697 TTAATTTAATTTTAT
1 ATAATTTAATTTAAT
52946712 ATAATT
1 ATAATT
52946718 AAATATATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTTAATTTAAT
Found at i:52947657 original size:18 final size:17
Alignment explanation
Indices: 52947636--52947693 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
52947626 AATTTTATAT
52947636 TTTATATTTAAAATAAAA
1 TTTATA-TTAAAATAAAA
52947654 TTTATATT--AAT--AA
1 TTTATATTAAAATAAAA
52947667 TTT-TATTAAAATAATAA
1 TTTATATTAAAATAA-AA
52947684 TTTATATTAA
1 TTTATATTAA
52947694 TTACATTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.12
13 5 0.15
14 3 0.09
15 3 0.09
17 7 0.21
18 12 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATATTAAAATAAAA
Found at i:52953431 original size:27 final size:27
Alignment explanation
Indices: 52953401--52953460 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
52953391 CAAACACATG
* *
52953401 ATGAACCGT-AAGGTGATAAGCTGCGAA
1 ATGAACCGTGAA-GTGACAAACTGCGAA
*
52953428 ATGAATCGTGAAGTGACAAACTGCGAA
1 ATGAACCGTGAAGTGACAAACTGCGAA
52953455 ATGAAC
1 ATGAAC
52953461 TATGAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (27 bp):
ATGAACCGTGAAGTGACAAACTGCGAA
Found at i:52953466 original size:27 final size:27
Alignment explanation
Indices: 52953421--52953472 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
52953411 AGGTGATAAG
* *
52953421 CTGCGAAATGAATCGTGAAGTGACAAA
1 CTGCGAAATGAATCATGAAATGACAAA
52953448 CTGCGAAATGAA-CTATGAAATGACA
1 CTGCGAAATGAATC-ATGAAATGACA
52953473 CAGTCAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (27 bp):
CTGCGAAATGAATCATGAAATGACAAA
Found at i:52954250 original size:33 final size:33
Alignment explanation
Indices: 52954208--52954279 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
52954198 GAATCAAAAT
* *
52954208 AGAGATTGACACGAGAGTTCATTACTAGTTCGG
1 AGAGATTGACACAAGAGTTAATTACTAGTTCGG
52954241 AGAGATTGACACAAGAGTTAATTACTAGTTCGG
1 AGAGATTGACACAAGAGTTAATTACTAGTTCGG
52954274 A-AGATT
1 AGAGATT
52954280 TTATGTCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 5 0.14
33 32 0.86
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (33 bp):
AGAGATTGACACAAGAGTTAATTACTAGTTCGG
Found at i:52955490 original size:10 final size:9
Alignment explanation
Indices: 52955475--52955515 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
52955465 AAAAAAAATA
52955475 TTATATTGTT
1 TTATATT-TT
52955485 TTATATTTT
1 TTATATTTT
52955494 TTAATATTTT
1 TT-ATATTTT
*
52955504 TAATATTTT
1 TTATATTTT
52955513 TTA
1 TTA
52955516 GTTATTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 13 0.46
10 15 0.54
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTATATTTT
Found at i:52955511 original size:19 final size:20
Alignment explanation
Indices: 52955477--52955515 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
52955467 AAAAAATATT
*
52955477 ATATTGTTTTATATTTTTTA
1 ATATTGTTTAATATTTTTTA
52955497 ATATT-TTTAATATTTTTTA
1 ATATTGTTTAATATTTTTTA
52955516 GTTATTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
ATATTGTTTAATATTTTTTA
Found at i:52957189 original size:247 final size:247
Alignment explanation
Indices: 52956850--52957344 Score: 981
Period size: 247 Copynumber: 2.0 Consensus size: 247
52956840 TAAGGTCAAG
52956850 TATATTTTTATAATATACTAAATATAATTATGTCAAATTATAAAATAAAATAATATTATATTATT
1 TATATTTTTATAATATACTAAATATAATTATGTCAAATTATAAAATAAAATAATATTATATTATT
52956915 TATTTTAATTATATAAATATTAATTAAATTTAACTAATTAAGTTGATAAAATAATAAAAAAGGGT
66 TATTTTAATTATATAAATATTAATTAAATTTAACTAATTAAGTTGATAAAATAATAAAAAAGGGT
52956980 TGTGACAAATTTAAGGATTCTTATAATTTCATCCCATTGTCTAATTAGGTTTACGGACGCATAAG
131 TGTGACAAATTTAAGGATTCTTATAATTTCATCCCATTGTCTAATTAGGTTTACGGACGCATAAG
*
52957045 AATAAGATTTAAGAGAAATTATATTAGACCTATCCATAGGTCAAGTAATCTA
196 AATAAGATTTAAGAGAAATTATATTAGACCTATCCATAGGTCAAGTAACCTA
52957097 TATATTTTTATAATATACTAAATATAATTATGTCAAATTATAAAATAAAATAATATTATATTATT
1 TATATTTTTATAATATACTAAATATAATTATGTCAAATTATAAAATAAAATAATATTATATTATT
52957162 TATTTTAATTATATAAATATTAATTAAATTTAACTAATTAAGTTGATAAAATAATAAAAAAGGGT
66 TATTTTAATTATATAAATATTAATTAAATTTAACTAATTAAGTTGATAAAATAATAAAAAAGGGT
52957227 TGTGACAAATTTAAGGATTCTTATAATTTCATCCCATTGTCTAATTAGGTTTACGGACGCATAAG
131 TGTGACAAATTTAAGGATTCTTATAATTTCATCCCATTGTCTAATTAGGTTTACGGACGCATAAG
52957292 AATAAGATTTAAGAGAAATTATATTAGACCTATCCATAGGTCAAGTAACCTA
196 AATAAGATTTAAGAGAAATTATATTAGACCTATCCATAGGTCAAGTAACCTA
52957344 T
1 T
52957345 TTAGTATATT
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 247 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.39
Consensus pattern (247 bp):
TATATTTTTATAATATACTAAATATAATTATGTCAAATTATAAAATAAAATAATATTATATTATT
TATTTTAATTATATAAATATTAATTAAATTTAACTAATTAAGTTGATAAAATAATAAAAAAGGGT
TGTGACAAATTTAAGGATTCTTATAATTTCATCCCATTGTCTAATTAGGTTTACGGACGCATAAG
AATAAGATTTAAGAGAAATTATATTAGACCTATCCATAGGTCAAGTAACCTA
Found at i:52963346 original size:24 final size:24
Alignment explanation
Indices: 52963309--52963362 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
52963299 AATTTCCACG
* *
52963309 ATTAACTTTGTATTACATAATGTT
1 ATTAATTTTATATTACATAATGTT
52963333 ATTAATTTTATATTACATAATGTT
1 ATTAATTTTATATTACATAATGTT
52963357 ATTAAT
1 ATTAAT
52963363 GATAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTAATTTTATATTACATAATGTT
Found at i:52963403 original size:18 final size:19
Alignment explanation
Indices: 52963380--52963418 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
52963370 AGATCTTTTT
52963380 TATTTTT-TATCAAAATAA
1 TATTTTTATATCAAAATAA
*
52963398 TATTTTTATATGAAAATAA
1 TATTTTTATATCAAAATAA
52963417 TA
1 TA
52963419 AATATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTTTATATCAAAATAA
Found at i:52967104 original size:23 final size:24
Alignment explanation
Indices: 52967073--52967120 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
52967063 CACTCAAAAC
52967073 ATTTGTTTTATTTTTTAAATTTTA
1 ATTTGTTTTATTTTTTAAATTTTA
52967097 ATTT-TTTTATTTTTTAAATTTTA
1 ATTTGTTTTATTTTTTAAATTTTA
52967120 A
1 A
52967121 AATACACCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (24 bp):
ATTTGTTTTATTTTTTAAATTTTA
Found at i:52967862 original size:18 final size:18
Alignment explanation
Indices: 52967839--52967873 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
52967829 TTAATAAATT
52967839 ATTAAAAACTATA-AAAAA
1 ATTAAAAA-TATAGAAAAA
52967857 ATTAAAAATATAGAAAA
1 ATTAAAAATATAGAAAA
52967874 TTGGTTCAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
ATTAAAAATATAGAAAAA
Found at i:52970709 original size:30 final size:30
Alignment explanation
Indices: 52970674--52970732 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
52970664 TATTTTATTG
*
52970674 TTAATTTTGTTATTATTTTAAAGGCATTTA
1 TTAATTTTGTTATTAATTTAAAGGCATTTA
*
52970704 TTAATTTTGTTATTAATTTAGAGGCATTT
1 TTAATTTTGTTATTAATTTAAAGGCATTT
52970733 GCTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTATTAATTTAAAGGCATTTA
Found at i:52976245 original size:20 final size:21
Alignment explanation
Indices: 52976212--52976250 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52976202 ACCCTCTTAT
*
52976212 CCAATGCTATAACT-ATAAGG
1 CCAATGCTAAAACTCATAAGG
*
52976232 CCAATGTTAAAACTCATAA
1 CCAATGCTAAAACTCATAA
52976251 AGTTAATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (21 bp):
CCAATGCTAAAACTCATAAGG
Found at i:52976583 original size:18 final size:18
Alignment explanation
Indices: 52976560--52976594 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52976550 TGGAAAGAGA
*
52976560 AAAGAATCATCAGGAAAG
1 AAAGAATCACCAGGAAAG
*
52976578 AAAGAATTACCAGGAAA
1 AAAGAATCACCAGGAAA
52976595 TCACACCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAGAATCACCAGGAAAG
Found at i:52978170 original size:17 final size:17
Alignment explanation
Indices: 52978125--52978173 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
52978115 AATACTATTT
*
52978125 TATTATTTTTTTGTTGT
1 TATTATTTTTTTGTTGC
* * *
52978142 TGTTGTTGTTTTGTTGC
1 TATTATTTTTTTGTTGC
*
52978159 TATTTTTTTTTTGTT
1 TATTATTTTTTTGTT
52978174 TTCTCACTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.06, C:0.02, G:0.16, T:0.76
Consensus pattern (17 bp):
TATTATTTTTTTGTTGC
Found at i:52979246 original size:16 final size:16
Alignment explanation
Indices: 52979225--52979258 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
52979215 CCCAAAAAAA
52979225 TTGAAATAAGAATTTT
1 TTGAAATAAGAATTTT
52979241 TTGAAATAAGAATTTT
1 TTGAAATAAGAATTTT
52979257 TT
1 TT
52979259 TTATTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
TTGAAATAAGAATTTT
Found at i:52979446 original size:5 final size:5
Alignment explanation
Indices: 52979425--52979482 Score: 53
Period size: 5 Copynumber: 10.6 Consensus size: 5
52979415 AAAGATAACT
* *
52979425 TGAATA TGAATA TGAAA TGAAA TGTAATT TGTAA TGAATA TGAAA TGAAA
1 TGAA-A TGAA-A TGAAA TGAAA TG-AA-A TGAAA TGAA-A TGAAA TGAAA
52979475 TGAAA TGA
1 TGAAA TGA
52979483 TGATTATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 25 0.56
6 18 0.40
7 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (5 bp):
TGAAA
Found at i:52979567 original size:40 final size:40
Alignment explanation
Indices: 52979491--52979568 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 40
52979481 GATGATTATG
* **
52979491 AAATGGAATAAAAGTTTAAATGAAAATAAATTATAAATTT
1 AAATGGAATAAAAGTTGAAATGAAAATAAAAAATAAATTT
52979531 AAAT-GAA-AAAAGTTGAAATGATAAATAAAAAAATAAAT
1 AAATGGAATAAAAGTTGAAATGA-AAAT-AAAAAATAAAT
52979569 AAAAATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 13 0.39
39 7 0.21
40 13 0.39
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (40 bp):
AAATGGAATAAAAGTTGAAATGAAAATAAAAAATAAATTT
Found at i:52979643 original size:33 final size:32
Alignment explanation
Indices: 52979577--52979646 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
52979567 ATAAAAATAG
* *
52979577 AAAATTTAAATTTAAATGAAATGAAATGTAAAT
1 AAAATTTAAATTCAAATGAAATGAAA-GAAAAT
52979610 AAAATTTAAAATTCAAATAGAAATGAAA-AAAAT
1 AAAATTT-AAATTCAAAT-GAAATGAAAGAAAAT
52979643 AAAA
1 AAAA
52979647 AAAGCTTGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 15 0.45
34 9 0.27
35 9 0.27
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (32 bp):
AAAATTTAAATTCAAATGAAATGAAAGAAAAT
Found at i:52979844 original size:22 final size:22
Alignment explanation
Indices: 52979797--52979838 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52979787 CATGTCAATT
* **
52979797 TTTTTTTTCATTTTTATTTACA
1 TTTTATTTCATTTAAATTTACA
52979819 TTTTATTTCATTTAAATTTA
1 TTTTATTTCATTTAAATTTA
52979839 AGTTTTCCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTTCATTTAAATTTACA
Found at i:52979887 original size:17 final size:18
Alignment explanation
Indices: 52979865--52979903 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52979855 TTATTTATTT
52979865 ATTTCACCTTTT-TTTTC
1 ATTTCACCTTTTATTTTC
**
52979882 ATTTCAGTTTTTATTTTC
1 ATTTCACCTTTTATTTTC
52979900 ATTT
1 ATTT
52979904 AAATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTTCACCTTTTATTTTC
Found at i:52980002 original size:20 final size:18
Alignment explanation
Indices: 52979972--52980023 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
52979962 TCAATTCATA
52979972 TTCATATTCAAGTTATCTTTT
1 TTCA-ATTCAA-TT-TCTTTT
*
52979993 TTCAATTCAATTTTTTTT
1 TTCAATTCAATTTCTTTT
52980011 TTCAATTC-ATTTC
1 TTCAATTCAATTTC
52980024 ATATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.14
18 13 0.45
19 2 0.07
20 6 0.21
21 4 0.14
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (18 bp):
TTCAATTCAATTTCTTTT
Found at i:52987189 original size:25 final size:25
Alignment explanation
Indices: 52987155--52987206 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52987145 ATACACAAAA
52987155 GAAAATTTTGAACTAGCGTTTCTGG
1 GAAAATTTTGAACTAGCGTTTCTGG
52987180 GAAAATTTTGAACTAGCGTTTCTGG
1 GAAAATTTTGAACTAGCGTTTCTGG
52987205 GA
1 GA
52987207 TTTTCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (25 bp):
GAAAATTTTGAACTAGCGTTTCTGG
Found at i:52990660 original size:13 final size:14
Alignment explanation
Indices: 52990637--52990670 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
52990627 TAAATTGGTG
52990637 AAATCTGGTAATAT
1 AAATCTGGTAATAT
52990651 AAAT-TGGTAATAT
1 AAATCTGGTAATAT
52990664 AAA-CTGG
1 AAATCTGG
52990671 CTCTATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (14 bp):
AAATCTGGTAATAT
Found at i:53000292 original size:29 final size:29
Alignment explanation
Indices: 53000271--53000344 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
53000261 AATGTGATTT
* *
53000271 TTATAAAAATAATATTAAAAATTAATTAA
1 TTATAAAAATAAAATAAAAAATTAATTAA
*
53000300 TTATAAAAATAAAATAAAAAAATAATTAA
1 TTATAAAAATAAAATAAAAAATTAATTAA
*
53000329 TTATGAAAATAAAATA
1 TTATAAAAATAAAATA
53000345 TTTATTATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (29 bp):
TTATAAAAATAAAATAAAAAATTAATTAA
Found at i:53000306 original size:17 final size:17
Alignment explanation
Indices: 53000286--53000338 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
53000276 AAAATAATAT
53000286 TAAAAATTAATTAATTA
1 TAAAAATTAATTAATTA
53000303 TAAAAA-TAA--AA-TA
1 TAAAAATTAATTAATTA
*
53000316 -AAAAAATAATTAATTA
1 TAAAAATTAATTAATTA
*
53000332 TGAAAAT
1 TAAAAAT
53000339 AAAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 2 0.07
15 2 0.07
16 5 0.17
17 10 0.34
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAAATTAATTAATTA
Found at i:53000339 original size:16 final size:16
Alignment explanation
Indices: 53000271--53000340 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 16
53000261 AATGTGATTT
53000271 TTATAAAAATAA-T-A
1 TTATAAAAATAATTAA
*
53000285 TTA-AAAATTAATTAA
1 TTATAAAAATAATTAA
53000300 TTATAAAAATAA--AA
1 TTATAAAAATAATTAA
*
53000314 -TAAAAAAATAATTAA
1 TTATAAAAATAATTAA
*
53000329 TTATGAAAATAA
1 TTATAAAAATAA
53000341 AATATTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 17 0.38
14 6 0.13
15 6 0.13
16 16 0.36
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (16 bp):
TTATAAAAATAATTAA
Found at i:53001222 original size:15 final size:16
Alignment explanation
Indices: 53001194--53001223 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53001184 TTTCTAAGTG
53001194 AACTACATTTTAATTA
1 AACTACATTTTAATTA
53001210 AACTACA-TTTAATT
1 AACTACATTTTAATT
53001224 GCAATAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (16 bp):
AACTACATTTTAATTA
Found at i:53012326 original size:18 final size:17
Alignment explanation
Indices: 53012303--53012345 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
53012293 GCAACAGTAA
53012303 AAAAAAACACTGAAAAAG
1 AAAAAAA-ACTGAAAAAG
*
53012321 AAAAAAAACTGAAAACG
1 AAAAAAAACTGAAAAAG
53012338 AAAAAAAA
1 AAAAAAAA
53012346 ATAAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.05
Consensus pattern (17 bp):
AAAAAAAACTGAAAAAG
Found at i:53012326 original size:19 final size:18
Alignment explanation
Indices: 53012302--53012346 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
53012292 CGCAACAGTA
53012302 AAAAAAAACACTGAAAAAG
1 AAAAAAAA-ACTGAAAAAG
*
53012321 -AAAAAAAACTGAAAACG
1 AAAAAAAAACTGAAAAAG
53012338 AAAAAAAAA
1 AAAAAAAAA
53012347 TAAAAAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (18 bp):
AAAAAAAAACTGAAAAAG
Found at i:53012351 original size:16 final size:17
Alignment explanation
Indices: 53012302--53012352 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
53012292 CGCAACAGTA
53012302 AAAAAAAACACTGAAAAAG
1 AAAAAAAA-A-TGAAAAAG
* *
53012321 AAAAAAAACTGAAAACG
1 AAAAAAAAATGAAAAAG
53012338 AAAAAAAAAT-AAAAA
1 AAAAAAAAATGAAAAA
53012353 ATGGGTCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
19 8 0.29
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (17 bp):
AAAAAAAAATGAAAAAG
Found at i:53013045 original size:16 final size:17
Alignment explanation
Indices: 53013024--53013067 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
53013014 TCCATTTTTT
53013024 ATTTTTTTTCGTTTTCA
1 ATTTTTTTTCGTTTTCA
*
53013041 ATTTTTTTTCTTTTTCA
1 ATTTTTTTTCGTTTTCA
53013058 ATATTTTTTT
1 AT-TTTTTTT
53013068 ACTGTTGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTTTTTTTCGTTTTCA
Found at i:53030908 original size:23 final size:23
Alignment explanation
Indices: 53030882--53030926 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
53030872 AAATAAAAAT
53030882 AATTAAAAAAAATAAATTTAAAC
1 AATTAAAAAAAATAAATTTAAAC
** * *
53030905 AATTTTAAAAAATTAGTTTAAA
1 AATTAAAAAAAATAAATTTAAA
53030927 TCTTATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAAAAAAATAAATTTAAAC
Found at i:53030959 original size:17 final size:17
Alignment explanation
Indices: 53030939--53030971 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53030929 TTATAAAATT
53030939 ATAAA-AATTGAAAATAA
1 ATAAACAATT-AAAATAA
53030956 ATAAACAATTAAAATA
1 ATAAACAATTAAAATA
53030972 TTTTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAACAATTAAAATAA
Found at i:53034807 original size:24 final size:24
Alignment explanation
Indices: 53034780--53034831 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53034770 TTAGTAAGTC
*
53034780 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
53034804 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
53034828 AAAT
1 AAAT
53034832 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:53035117 original size:7 final size:7
Alignment explanation
Indices: 53035101--53035134 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
53035091 TTTTTTTAAT
53035101 TTAAACC
1 TTAAACC
*
53035108 TTATACC
1 TTAAACC
*
53035115 TTAGACC
1 TTAAACC
53035122 TTAAACC
1 TTAAACC
53035129 TTAAAC
1 TTAAAC
53035135 TCAAAACTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.32
Consensus pattern (7 bp):
TTAAACC
Found at i:53039424 original size:38 final size:38
Alignment explanation
Indices: 53039373--53039765 Score: 540
Period size: 38 Copynumber: 10.3 Consensus size: 38
53039363 ATATTCGAAG
*
53039373 TATATCAGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
53039411 TATATCCAGGTTAAATCCCGCAGGCTTCGT-CTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* ** *
53039448 TATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
*
53039488 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
53039526 TATATCCAGGTTAAATCCCGCAGGCTTCGT-CTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* ** *
53039563 TATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
*
53039603 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
53039641 TATATCCAGGTTAAATCCCGCAGGCTTCGT-CTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* ** *
53039678 TATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
*
53039718 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
53039756 TATATCCGGG
1 TATATCCGGG
53039766 AGGCTATAAT
Statistics
Matches: 309, Mismatches: 37, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
37 48 0.16
38 165 0.53
39 51 0.17
40 45 0.15
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:53039485 original size:77 final size:76
Alignment explanation
Indices: 53039373--53039765 Score: 522
Period size: 77 Copynumber: 5.1 Consensus size: 76
53039363 ATATTCGAAG
* * * *
53039373 TATATCAGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAAACCCACAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTT
53039438 CGT-CTGGTAT
66 CGTGCTGGTAT
* **
53039448 TATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGC
1 TATATCCGGG-TTAAA-ACCCACAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGC
53039513 TTCGTGCTGGTAT
64 TTCGTGCTGGTAT
* * * * **
53039526 TATATCCAGGTTAAATCCCGCAGGCTTCGT-CTGGTATTATATCCGGGCTTAAAGACCTACAGGC
1 TATATCCGGGTTAAAACCCACAGGCTTCGTGCTGGTATTATATCCGGG-TTAAA-TCCCGCAGGC
*
53039590 TTCGTGCTGGTAA
64 TTCGTGCTGGTAT
* * * *
53039603 AATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTT
1 TATATCCGGGTTAAAACCCACAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTT
53039668 CGT-CTGGTAT
66 CGTGCTGGTAT
* **
53039678 TATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGC
1 TATATCCGGG-TTAAA-ACCCACAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGC
53039743 TTCGTGCTGGTAT
64 TTCGTGCTGGTAT
53039756 TATATCCGGG
1 TATATCCGGG
53039766 AGGCTATAAT
Statistics
Matches: 278, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
75 39 0.14
76 39 0.14
77 151 0.54
78 49 0.18
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (76 bp):
TATATCCGGGTTAAAACCCACAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTT
CGTGCTGGTAT
Found at i:53039576 original size:115 final size:115
Alignment explanation
Indices: 53039374--53039762 Score: 769
Period size: 115 Copynumber: 3.4 Consensus size: 115
53039364 TATTCGAAGT
*
53039374 ATATCAGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
53039439 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
66 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
53039489 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
53039554 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
66 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
53039604 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
53039669 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
66 GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
53039719 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCC
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCC
53039763 GGGAGGCTAT
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 273 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (115 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCAGGTTAAATCCCGCAGGCTTC
GTCTGGTATTATATCCGGGCTTAAAGACCTACAGGCTTCGTGCTGGTAAA
Found at i:53040824 original size:7 final size:7
Alignment explanation
Indices: 53040812--53040838 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53040802 ACCCATTACA
53040812 ACCCAAT
1 ACCCAAT
53040819 ACCCAAT
1 ACCCAAT
53040826 ACCCAAT
1 ACCCAAT
53040833 ACCCAA
1 ACCCAA
53040839 ATTTCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.11
Consensus pattern (7 bp):
ACCCAAT
Found at i:53040840 original size:45 final size:44
Alignment explanation
Indices: 53040789--53040875 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 44
53040779 AAACAACCTC
* * *
53040789 CCCAAATCCCTAAACCCATTACAACCCAATACCCAATACCCAATA
1 CCCAAATCCCTAAACCCATGAAAACCCAAAACCCAA-ACCCAATA
** *
53040834 CCCAAATTTCTAAATCCATGAAAACCCAAAACCCAAACCCAA
1 CCCAAATCCCTAAACCCATGAAAACCCAAAACCCAAACCCAA
53040876 CAGACTTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 6 0.17
45 30 0.83
ACGTcount: A:0.45, C:0.39, G:0.01, T:0.15
Consensus pattern (44 bp):
CCCAAATCCCTAAACCCATGAAAACCCAAAACCCAAACCCAATA
Found at i:53041342 original size:6 final size:7
Alignment explanation
Indices: 53041325--53041351 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53041315 TAAAAGCATA
53041325 AAAAAAT
1 AAAAAAT
53041332 AAAAAAT
1 AAAAAAT
53041339 AAAAAAT
1 AAAAAAT
53041346 AAAAAA
1 AAAAAA
53041352 GGCCTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:53041762 original size:3 final size:3
Alignment explanation
Indices: 53041756--53041986 Score: 89
Period size: 3 Copynumber: 77.0 Consensus size: 3
53041746 TATTTTTTAA
* * *
53041756 TAT TAT TAA TAT TAT TAC TAT TAT TTT TAT T-T CTAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* ** * * * * * *
53041801 TAC CGT TAG TAT TAT T-T TCAT TAC TCT TAT TTT TAT TAA CA- TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
53041845 TAT TACT AAT TTT TAC CA- TAT TAT TAT T-T T-T TA- TGT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
53041887 TGT TAT TAA CAT ATAT TAT TGT TAT TAACG TAC TAA TAT TTT CTAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT T-A-T TAT TAT TAT TAT -TAT TAT
* * * *
53041936 TAT TAT TAT TAC TAA TAT CAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53041984 TAT
1 TAT
53041987 ATTTCCTTTT
Statistics
Matches: 162, Mismatches: 53, Indels: 26
0.67 0.22 0.11
Matches are distributed among these distances:
2 10 0.06
3 140 0.86
4 11 0.07
5 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:53042170 original size:3 final size:3
Alignment explanation
Indices: 53042164--53042299 Score: 73
Period size: 3 Copynumber: 45.0 Consensus size: 3
53042154 ATTATCTGTT
* * * *
53042164 TTA TTA TTA TTA TTA TT- TGTA TTTA TCA TTA TTA TCA CTA TTA TTT
1 TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
53042210 TTA TTT TTA TTA CTA TTA TCA TTT TTA -AA TTA TTA TTA CTA TTA TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
53042257 TT- TTA CCTT- TTA ATA CATA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA --TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
53042300 GTGTACGTTT
Statistics
Matches: 99, Mismatches: 25, Indels: 18
0.70 0.18 0.13
Matches are distributed among these distances:
2 6 0.06
3 85 0.86
4 5 0.05
5 3 0.03
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Done.